Whups, I suppose I forgot to explain the second half but it belongs in its own thread. See, even if your soldiers are able to use every bit of equipment at any time. No one ever said they knew how. Experience is what counters this whole system.
Think of it this way. You have 3 playing cards in your hand and a pair of scissors in the other. The first card you cut into a triangle, the second card you cut into a circle, and the third card you leave alone. When you hold these in your hand you have a balanced set of shapes. The enemy you are fighting slaps down a circle, to counter that you put down your triangle. He then puts down a square, and you counter with your uncut rectangle card. Then he puts down an oval. This results in a problem, an oval is countered by a diamond, but the only card you have left is a circle.
Under a system of hard counters you just lost this game. You don't have an A to beat his B. However a soft counter system works out a bit differently. See you still have the scissors in your other hand. You take the circle and cut it into a diamond shape and use it to counter the oval set down by your enemy. At this point you have a 50/50 chance of victory. Why? See when you cut that circle into a diamond, the shape you end up with is smaller than the one you would have gotten had you used the uncut card to make the diamond instead. Even thought "diamond beats oval", your diamond is only half of its regular size. This is enough to counter the enemy oval 1-1 but not enough to give it the usual advantage.
The size of the cards represent experience. You can only know so much at one time. It is not possible to know everything. Skills that are not used will degrade, become rusty and eventually will be lost. You CAN toggle a bunch of switches and turn your units into the "perfect" counter to your enemy. But when you do this you end up with inexperienced troops facing off against experienced specialized soldiers.
If you had 20 swordsmen facing off against 20 archers. You can put them on horses none of them have ridden before and send them to attack. But they will still lose against the archers because the archers took the time to dig hidden pit traps. More experienced cavalry would *never* fall for such a simple trick.
Using the starcraft example again. The toggle switch when you build the unit controls what weapon they will have when they leave the barracks. When a unit is new or "green" it will have a 50/50 split in terms of skills between the rifle and flamethrower. These are marines after all and they would know how to use the entire armoury at their disposal. When you send marine riflemen into combat they would build up experience. The longer they survive and use a rifle the higher thier rifle skill will get. This comes at the detriment of thier flamethrower skills. In this case the skills would cap out at 75% rifle and 25% Flame.
Suddenly a horde of zerglings appear on the horizon. At this point you have the option of returning to base and rearming all of your riflemen with flamethrowers instead. But that would be a bad idea because thier flamethrower skills are lacking and they will start to lose the high degree of skill they built up with rifles.
So as you can see, even if you can change your soldiers to fit every single situation. It is still very important to start with and maintain a proper balance between the soldiers under your command. It is possible to give soldiers a completetly unfamiliar weapon or send them into situations they are not trained for. But these instances should be considered desperate measures, completetly viable yes but your strategy should not be based solely upon them.